TBOB - Text based Blast Output Browser
--------------------------------------
The tbob program for browsing the output from BLAST and retrieving sequences
is now available to all.
What is it?
~~~~~~~~~~~
TBOB is a Blast Output Browser. BLAST (Basic Local Alignment
Search Tool) is the search algorithm employed by the blast programs
blastn and blastp, for example, for searching nucleotide or protein
sequences against their respective databases.
Output from the blast programs can be difficult to read, especially
when there are many search results to be analysed, each potentially
with many matches with sequences in the database. The output from blast
is usually a long text file with information spread throughout it; as a
consequence, viewing this output can be difficult and inconvenient. TBOB
solves this problem by only showing parts of the blast output at any time,
letting the user jump from one place to another using simple one-keystroke
commands.
TBOB also permits retrieval of sequences from the NCBI retrieve email
server, so that interesting sequences can be obtained for further analysis.
This is particularly convenient as it can be performed while the blast
results are being viewed.
TBOB has a character-based interface, and therefore no special graphical
capabilities are needed.
Platforms/Operating Systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbob will run on UNIX systems with a perl interpreter installed.
Obtaining tbob
~~~~~~~~~~~~~~
tbob can be obtained by gopher by pointing your gopher client at:
megasun.bch.umontreal.ca
and selecting:
--> 5. Computational Molecular Biology- programs, documents, help/
--> 8. Databases/
--> 1. Blast/
--> 1. tbob- text based application to browse blast output/
or by anonymous ftp to:
megasun.bch.umontreal.ca
Files can be retrieved from the /pub/tbob directory.
Installation Instructions
~~~~~~~~~~~~~~~~~~~~~~~~~
Installation instructions can be found at the above sites in the
INSTALLATION document. Also see the document getting.perl (also
located in these archives) if you do not have access to perl on your
system.
Further Information
~~~~~~~~~~~~~~~~~~~
For more information about the tbob project, send email to the
Informatics Division of the Organelle Genome Megasequencing Unit
at the Universite de Montreal:
ogmp at bch.umontreal.ca
All feedback welcome.
Credits
~~~~~~~
This software was written by Pierre Rioux of the OGMP (Organelle
Genome Megasequencing Project), Departement de Biochimie, Universite
de Montreal (riouxp at bch.umontreal.ca) under the management of Tim
Littlejohn, OGMP, Departement de Biochimie, Universite de Montreal
(tim at bch.umontreal.ca). Please send any comments/correspondence to
ogmp at bch.umontreal.ca.
The development of tbob was supported by a grant from the Canadian
Genome Analysis and Technology Program (CGAT).
--
==============================================================================
Tim Littlejohn
E-mail: tim at bch.umontreal.ca
Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149
Universite de Montreal Fax: (514) 343-2210
C.P. 6128, Centre-ville
Montreal (Quebec), H3C 3J7
CANADA
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